The long-term goals of our laboratory are to understand how noncoding RNAs function, how cells recognize and degrade defective and unneeded RNAs, and how failure to degrade these RNAs affects cell function and contributes to human disease. Our current experiments focus on three areas: 1) defining roles for Ro60 ribonucleoproteins in mammalian cells and bacteria, 2) elucidating the roles of RNA surveillance pathways in mammalian cell physiology, and 3) determining how cellular noncoding RNAs contribute to replication of the human immunodeficiency virus HIV-1 and other retroviruses. To define roles for Ro60 in mammalian cells, we combined high-throughput sequencing of RNA after in vivo crosslinking and immunoprecipitation (HITS-CLIP) with transcriptome analyses (RNA-Seq). Using this approach, we identified specific RNAs that require Ro60 for their degradation. We also identified RNAs that require Ro60 for their stable accumulation. The mechanisms by which Ro60 assists in the biogenesis and decay of these RNAs is under investigation. We are also examining the extent to which Ro60-bound noncoding RNAs, called Y RNAs, are involved in these processes. In bacteria, our recent experiments have been carried out in the genetically tractable Salmonella enterica serovar Typhimurium (S. Typhimurium), an enteric bacterium closely related to Escherichia coli. In S. Typhimurium and many other bacteria, Ro60 and Y RNAs are part of a highly regulated RNA repair operon that also includes the RtcB RNA ligase. We are dissecting both the ways in which this operon is regulated and the roles of Ro60 and Y RNAs in S. Typhimurium. In our second focus, we have shown that the multiprotein nuclease complex known as the RNA exosome is important for maintaining the unique properties of human embryonic stem cells. Finally, our retroviral studies identified the set of noncoding RNAs within HIV-1 virions. We collaborated with the laboratory of Sanford Simon (Rockefeller University) to visualize the packaging of an abundant host cell noncoding RNA, the 7SL subunit of the signal recognition particle, into virions. These studies revealed that 7SL binds the viral structural protein Gag in the cytosol and accumulates with Gag at sites of viral assembly. The experiments to characterize the noncoding RNAs packaged by HIV-1, their mechanism of recruitment and their function in the HIV-1 lifecycle could identify new therapeutic targets.